Identifying the phase diagram structure for optimal information integration in morphogen systems

TL;DR

This paper uses an optimality-based top-down approach to analyze gene regulatory networks in morphogen systems, revealing that phase diagram structure is crucial for optimal information integration and accurately predicting pattern shifts in fly embryos.

Contribution

It introduces a phase diagram-focused analysis for understanding GRN function, providing a new perspective beyond traditional topological methods.

Findings

Optimal integration strategy depends on phase diagram structure.

Model accurately predicts pattern shifts in fly embryo morphogen Bicoid.

Highlights importance of phase diagrams over network topology.

Abstract

Gene regulatory networks (GRNs) perform a wide range of biological functions. It is, however, often challenging to reveal their functioning mechanism with the conventional approach focusing on the network topological structure from a bottom-up perspective. Here, we apply the top-down approach based on the optimality theory to study the information integration in morphogen systems, and show that the optimal integration strategy raises requirement on the phase diagram, rather than the topological structure, of a GRN. For the morphogen system in early fly embryos, our parameter-free model can quantitatively predict the patterning position shifts upon the dosage change of the morphogen Bicoid.